Method for providing dna fragments derived from an archived sample

Abstract

Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc.). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.

What is claimed is: 
     
         1 . A method for amplifying DNA derived from an archived sample, comprising amplifying DNA in a DNA amplification step comprising use of at least one DNA amplification parameter selected from the group consisting of: a polymerase concentration in the range of about 0.05 to about 0.3 U/μl; a concentration of each nucleotide in the range of about 200 to about 800 μmol/l; and a time of an elongation step in the range of about 0.1 to about 1.0 s/bp. 
     
     
         2 . The method of  claim 1 , wherein the DNA amplification step comprises at least one DNA amplification parameter selected from the group consisting of: a polymerase concentration of about 0.15 U/μl; a concentration of each nucleotide of about 400 μmol/l; and a time of an elongation step of about 0.5 s/bp. 
     
     
         3 . A test kit for carrying out the method according to  claim 1 , comprising:
 a container;   organic solvents for removal of paraffin;   proteinase K, buffer for lysis, or both;   solutions for DNA extraction, devices for DNA extraction, or both;   solutions for bisulfite treatment, devices for bisulfite treatment, or both;   solutions for DNA purification, devices for DNA purification, or both;   solutions for DNA amplification, substances for DNA amplification, or both; and   a manual for carrying out the method, a description for carrying out the method, or both.   
     
     
         4 . A test kit for carrying out the method according to  claim 2 , comprising:
 a container;   organic solvents for removal of paraffin;   proteinase K, buffer for lysis, or both;   solutions for DNA extraction, devices for DNA extraction, or both;   solutions for bisulfite treatment, devices for bisulfite treatment, or both;   solutions for DNA purification, devices for DNA purification, or both;   solutions for DNA amplification, substances for DNA amplification, or both; and   a manual for carrying out the method, a description for carrying out the method, or both.